Urgent request - Pipeline for finding somatic and germline mutations of a cancer patient

Question

[Whoknows]

Hi all, This project belong to a patient and I need some fast helps for the analysis

I have 2 WES samples from him, one of is Blood WES and another is cancer tissue WES. I just wanted to find germline mutation from Blood exome and also somatic mutation by comparing Blood and Cancer tissue samples, and finally finding relation among cancer genes with those mutations using annovar or other related tools.

First, I need to check my pipeline for blood (germline mutations):

After running Picard-MarkDuplicates I have ran BaseRecalibrator, PrintReads and HaplotypeCaller and VQSR and then running Annovar, Is it correct?

Second step finding somatic variations related to tumor tissue, what pipeline I should apply? ( I could not find exact pipeline from GATK website)

My third question is which tool I should used for find relation among variation and cancer related genes.

Thanks for your helps.

Answer 1

[TriS]

a little bit of disclaimer first, just for safety: here we do NOT provide information that lead to choosing or altering a medical treatment, all info are for educational purpose and the investigator assumes the final responsibility of what to do with the info provided.

that said...what you did in the first step is the "preprocessing" of the samples that is described in the best practices from GATK, and that's good. for the second step there are a number of tools that will call somatic mutations from pairing blood/germline/control and tumor WES. MuTect2, Varscan2, Strelka are three of the most common used one. all tools have their pros-cons, I normally run three and filter data after that.

for your third question you can use COSMIC or PharmGKB to see whether the variants that you find are known or known to associate with drug metabolism

[Whoknows]

dear TriS thanks for your post, is was very constructive to me.